Test Code: 2159

CNTNAP2-related Disorders: CNTNAP2 Gene Sequencing
Test Code: 2159
Turnaround time: 5 weeks

CONDITION DESCRIPTION

Pitt-Hopkins-Like Syndrome-1
Pitt-Hopkins-like syndrome-1 and Pitt-Hopkins-like syndrome-2 are inherited in an autosomal recessive manner and are caused by mutations in the genes CNTNAP2 (7q35) and NRXN1 (2p16.3) respectively. Both of these conditions resemble Pitt-Hopkins syndrome, caused by mutation of the TCF4 gene, with regard to the distinctive facial features, severe intellectual disability and breathing abnormalities; however, there is a phenotypical difference. While speech is severely impaired, individuals with mutation the CNTNAP2 or NRXN1 gene have normal or mildly delayed motor milestones.

Please note that this test is for the CNTNAP2 gene only.

Cortical Dysplasia-Focal Epilepsy Syndrome
In Old Order Amish children, Strauss et al. (2006) identified a homozygous mutation of the CNTNAP2 gene (7q35-q36) that causes focal epilepsy, cortical dysplasia, reduced deep-tendon reflexes, and relative macrocephaly. The focal seizures begin in early childhood and do not respond to therapy. After the onset of seizures, language regression, hyperactivity, intellectual disability, and impulsive and aggressive behavior are observed.

For patients with suspected CNTNAP2-related disorders, sequence analysis is recommended as the first step in mutation identification. For patients in whom mutations are not identified by full gene sequencing, deletion/duplication analysis is appropriate.

References:
• OMIM #604569: CNTNAP2 gene
• OMIM #610042: Cortical Dysplasia-Focal Epilepsy syndrome
• OMIM #610954: PTHS
• Zweier et al. (2009) Am J Hum Genet, 85:655-666.
• Stauss et al. (2006). N Engl J Med; 354:1370-1377.

GENES
CNTNAP2

INDICATIONS
This test is indicated for:

  • Confirmation of a clinical diagnosis of CNTNAP2-related disorders.
  • Carrier testing in adults with a family history of CNTNAP2-related disorders.

METHODOLOGY

Next Generation Sequencing: In-solution hybridization of all coding exons is performed on the patient’s genomic DNA. Although some deep intronic regions may also be analyzed, this assay is not mean to interrogate most promoter regions, deep intronic regions, or other regulatory elements, and does not detect single or multi-exon deletions or duplications. Direct sequencing of the captured regions is performed using next generation sequencing. The patient’s gene sequences are then compared to a standard reference sequence. Potentially causative variants and areas of low coverage are Sanger-sequenced. Sequence variations are classified as pathogenic, likely pathogenic, benign, likely benign, or variants of unknown significance. Variants of unknown significance may require further studies of the patient and/or family members.

DETECTION

Clinical Sensitivity: Unknown. Mutations in the promoter region, some mutations in the introns and other regulatory element mutations cannot be detected by this analysis. Large deletions will not be detected by this analysis. Results of molecular analysis should be interpreted in the context of the patient’s clinical and/or biochemical phenotype.

Analytical Sensitivity: ~99%

SPECIMEN REQUIREMENTS

Submit only 1 of the following specimen types
* Preferred specimen type: Whole Blood

Type: Whole Blood
Specimen Requirements:
In EDTA (purple top) or ACD (yellow top) tube: Infants (2 years): 3-5 ml
Older Children & Adults: 5-10 ml

Specimen Collection and Shipping: Refrigerate until time of shipment. Ship sample within 5 days of collection at room temperature with overnight delivery.

Type: Saliva
Specimen Requirements:
OrageneTM Saliva Collection kit (available through CEN4GEN) used according to manufacturer instructions.

Specimen Collection and Shipping: Store sample at room temperature. Ship sample within 5 days of collection at room temperature with overnight delivery.

RELATED TESTS

• Deletion/duplication analysis of the CNTNAP2 gene by CGH array is available for those individuals in whom sequence analysis is negative.
• Sequencing and deletion/duplication analysis of the TCF4 and NRXRN1 genes are available.
• Custom diagnostic mutation analysis (test code: 6875) is available to family members if mutations are identified by targeted mutation testing or sequencing analysis.